Whenever MTune detects an "tune problem", the configuration problem detected! text label will blink in red to notify the user of an issue that needs to be taken cared of.

In the above example, MTune detects an error caused by setting 2 inputs as the the same source, in this case two vehicle speed (front), which can cause all kind of weird problem, as you might imagine...
•Ignition cylinder angle trim problem.
•Memory almost full / fragmented.
•No secondary injector outputs
•Output function used on more than 4 outputs.
•Output set on an unavailable output
•Primary injector flow tracking has an invalid value
•No secondary injector outputs.
•Pulse function used on 2 inputs.
•Wasted spark not supported on 1 cylinder engines
Configuration problems detected and how to solve them